behavResources.mat - MobsLab/PreProcessing GitHub Wiki

This post gives a description of the variables that are common to all experiments and that can be found in behavResources.mat

Tracking variables to use

Xtsd / Ytsd : Instantaneous position in tsd format
Vtsd : Instantaneous speed in tsd format, derived from Xtsd and Ytsd
MovAcctsd : Movement derived from 3 accelerometer channels recorded by Intan headstage
Imdifftsd : Number of pixels that changes between two successive frames, gives could idea of quantity of movement of mouse
FreezeEpoch : IntervalSet of freezing episodes, defined using a threshold on Imdifftsd
FreezeAccEpoch : IntervalSet of freezing episodes, defined using a threshold on MovAcctsd

Original tracking variables

PosMat / PosMatInit : Matrix with 4 entries : time, x-position, y-position, stimulation timestamps (optional, depends on code). PosMatInit is the original values derived online during tracking, PosMat has been interpolated and corrected.
ImDiff / ImDiffInit : Matrix with 4 entries : time, average pixel-wise change, number of pixels used to calculate the pixel-wise change (is defined by SrdZone if mouse i.e. located, otherwise down over all image)

Tracking parameters

ref : reference image used for tracking
mask : area in which mouse can be found
Ratio_IMAonREAL : ratio between pixels from the video and real cm
SrdZone : size of zone around center of mouse used to calculate pixel-wise change
strsz : size of object used for object erosion and dilation
th_immob : threshold applied to im_diff to define freezing epochs thtps_immob : minimum duration of a freezing event for im_diff th_immob_Acc : threshold applied to MovAcctsd to define freezing epochs thtps_immob_Acc : minimum duration of a freezing event for accelero